Coverage for /builds/kinetik161/ase/ase/db/convert.py: 17.39%

1import optparse 

2import os 

3 

4import numpy as np 

5 

6from ase.db import connect 

7from ase.db.sqlite import index_statements 

8 

9 

10def convert(name, opts): 

11 con1 = connect(name, use_lock_file=False) 

12 con1._allow_reading_old_format = True 

13 newname = name[:-2] + 'new.db' 

14 with connect(newname, create_indices=False, use_lock_file=False) as con2: 

15 row = None 

16 for row in con1.select(): 

17 kvp = row.get('key_value_pairs', {}) 

18 if opts.convert_strings_to_numbers: 

19 for key, value in kvp.items(): 

20 if isinstance(value, str): 

21 try: 

22 value = float(value) 

23 except ValueError: 

24 pass 

25 else: 

26 kvp[key] = value 

27 if opts.convert_minus_to_not_a_number: 

28 for key, value in kvp.items(): 

29 if value == '-': 

30 kvp[key] = np.nan 

31 

32 atoms = row.toatoms() 

33 if opts.remove_constrints: 

34 atoms.constraints = [] 

35 con2.write(atoms, data=row.get('data'), **kvp) 

36 

37 assert row is not None, 'Your database is empty!' 

38 

39 c = con2._connect() 

40 for statement in index_statements: 

41 c.execute(statement) 

42 c.commit() 

43 

44 os.rename(name, name[:-2] + 'old.db') 

45 os.rename(newname, name) 

46 

47 

48def main(): 

49 parser = optparse.OptionParser() 

50 parser.add_option('-S', '--convert-strings-to-numbers', 

51 action='store_true') 

52 parser.add_option('-N', '--convert-minus-to-not-a-number', 

53 action='store_true') 

54 parser.add_option('-C', '--remove-constraints', 

55 action='store_true') 

56 opts, args = parser.parse_args() 

57 for name in args: 

58 convert(name, opts) 

59 

60 

61if __name__ == '__main__': 

62 main()